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WO2024124181A3 - Compositions and methods for detecting homologous recombination - Google Patents

Compositions and methods for detecting homologous recombination Download PDF

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Publication number
WO2024124181A3
WO2024124181A3 PCT/US2023/083199 US2023083199W WO2024124181A3 WO 2024124181 A3 WO2024124181 A3 WO 2024124181A3 US 2023083199 W US2023083199 W US 2023083199W WO 2024124181 A3 WO2024124181 A3 WO 2024124181A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
homologous recombination
compositions
detecting homologous
detecting
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2023/083199
Other languages
French (fr)
Other versions
WO2024124181A2 (en
Inventor
Ruolin LIU
Viktor ADALSTEINSSON
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Broad Institute Inc
Original Assignee
Broad Institute Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Broad Institute Inc filed Critical Broad Institute Inc
Publication of WO2024124181A2 publication Critical patent/WO2024124181A2/en
Publication of WO2024124181A3 publication Critical patent/WO2024124181A3/en
Priority to US19/231,368 priority Critical patent/US20250372258A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

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  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Medical Informatics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Public Health (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biomedical Technology (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Primary Health Care (AREA)
  • Pathology (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

The disclosure provides compositions and methods for detecting Homologous Recombination Deficiency (HRD) in biological samples (e.g., liquid biopsies, tissue samples) of a subject.
PCT/US2023/083199 2022-12-09 2023-12-08 Compositions and methods for detecting homologous recombination Ceased WO2024124181A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US19/231,368 US20250372258A1 (en) 2022-12-09 2025-06-06 Computational framework for enhancing a signal-to-noise ratio (snr) in processing noisy read signals

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263431572P 2022-12-09 2022-12-09
US63/431,572 2022-12-09

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US19/231,368 Continuation-In-Part US20250372258A1 (en) 2022-12-09 2025-06-06 Computational framework for enhancing a signal-to-noise ratio (snr) in processing noisy read signals

Publications (2)

Publication Number Publication Date
WO2024124181A2 WO2024124181A2 (en) 2024-06-13
WO2024124181A3 true WO2024124181A3 (en) 2024-07-18

Family

ID=91380350

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/083199 Ceased WO2024124181A2 (en) 2022-12-09 2023-12-08 Compositions and methods for detecting homologous recombination

Country Status (2)

Country Link
US (1) US20250372258A1 (en)
WO (1) WO2024124181A2 (en)

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20210262016A1 (en) * 2018-11-13 2021-08-26 Myriad Genetics, Inc. Methods and systems for somatic mutations and uses thereof
US20210343419A1 (en) * 2020-04-09 2021-11-04 Tempus Labs, Inc. Predicting likelihood and site of metastasis from patient records
US20210350904A1 (en) * 2018-10-17 2021-11-11 Tempus Labs, Inc. Data-based mental disorder research and treatment systems and methods
US20220028481A1 (en) * 2020-07-27 2022-01-27 Sophia Genetics S.A. Methods for identifying chromosomal spatial instability such as homologous repair deficiency in low coverage next-generation sequencing data
US20220025468A1 (en) * 2020-05-14 2022-01-27 Guardant Health, Inc. Homologous recombination repair deficiency detection

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20210350904A1 (en) * 2018-10-17 2021-11-11 Tempus Labs, Inc. Data-based mental disorder research and treatment systems and methods
US20210262016A1 (en) * 2018-11-13 2021-08-26 Myriad Genetics, Inc. Methods and systems for somatic mutations and uses thereof
US20210343419A1 (en) * 2020-04-09 2021-11-04 Tempus Labs, Inc. Predicting likelihood and site of metastasis from patient records
US20220025468A1 (en) * 2020-05-14 2022-01-27 Guardant Health, Inc. Homologous recombination repair deficiency detection
US20220028481A1 (en) * 2020-07-27 2022-01-27 Sophia Genetics S.A. Methods for identifying chromosomal spatial instability such as homologous repair deficiency in low coverage next-generation sequencing data

Also Published As

Publication number Publication date
US20250372258A1 (en) 2025-12-04
WO2024124181A2 (en) 2024-06-13

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